/// <summary> /// Reads rna, peptide Fasta-Sequence(s) and generates HELMNotation /// </summary> /// <param name="fastaString"></param> /// <returns></returns> public static string FastaToHelm(string fastaString) { string helm = null; string errorMsg = "Can't convert FASTA to Helm"; if (UseWebEditor) { throw new InvalidCastException(errorMsg); // can't do yet } else { string helm1 = HelmService.GenerateHELMFromFastaPeptide(fastaString); if (helm1 == null) { throw new InvalidCastException(errorMsg); } string helm2 = HelmService.GenerateHELMFromFastaRNA(fastaString); if (helm2 == null) { throw new InvalidCastException(errorMsg); } if (helm1.Length >= helm2.Length) { return(helm1); } else { return(helm2); } } }
/// <summary> /// Reads HELMNotation and converts it into peptide/RNA analogue (natural) sequence /// </summary> /// <param name="helm"></param> /// <returns></returns> public static string HelmToAnalogSequence(string helm) { string seq = null; if (UseWebEditor) { Browser.SetHelm(helm); seq = Browser.GetSequence(); } else { if (IsPeptideString(helm)) { seq = HelmService.ConvertIntoPeptideAnalogSequence(helm); } else if (IsRnaString(helm)) { seq = HelmService.ConvertIntoRNAAnalogSequence(helm); } } return(seq); }
/// <summary> /// Converts HELM Input into Fasta (RNA or Peptide) /// <param name="helm"></param> /// <returns></returns> public static string HelmToFastaString(string helm) { string fasta = null; if (UseWebEditor) { return("Can't convert Helm to FASTA"); } else { fasta = HelmService.GenerateFastaFromHelm(helm); } return(fasta); }
public static string FastaRnaToHelm(string fastaString) { string helm = null; if (UseWebEditor) { throw new InvalidCastException("Can't convert FASTA to Helm"); // can't do yet } else { helm = HelmService.GenerateHELMFromFastaRNA(fastaString); } return(helm); }
/// <summary> /// SMILES generation for the whole HELM molecule /// </summary> /// <param name="helm"></param> /// <returns></returns> public static string HelmToSmiles( MoleculeMx mol, string helm) { string smiles = null; if (UseWebEditor && DebugMx.False) // don't use this, only gets molfile at monomer level, not atoms/bonds { Browser.SetHelm(helm); smiles = Browser.GetSmiles(); } else { smiles = HelmService.GenerateSMILESForHELM(helm); } return(smiles); }
/// <summary> /// Reads RNA / peptide sequence and generates HELMNotation /// </summary> /// <param name="sequenceString"></param> /// <returns></returns> public static string SequenceToHelm(string seqString) { string helm = null; if (UseWebEditor) { throw new InvalidCastException("Can't convert sequence to Helm"); // can't do yet } else { if (IsPeptideString(seqString)) { helm = HelmService.GenerateHELMFromPeptideSequence(seqString); } else { helm = HelmService.GenerateHELMFromRnaSequence(seqString); } } return(helm); }
public static string FastaPeptideToHelm(string fastaString) { string helm = HelmService.GenerateHELMFromFastaPeptide(fastaString); return(helm); }